Origin IGS: taaaaggttattgggtgtttgggtattgatataccgtatatacgctcatattgggcgtatatacaacccaatacctctatgccgaaagttgcattagtttttgaataataaaaggttagatatatgtacacgaaacaaaaatataataccgatgttctctgtcaccgttcgatacggttgtgcggatagttggctttgtctacaaagcattttatgcgtgagttcttacgaacggagcggttggattgtctggacggaaaaacgtttcccctgccccaaaacaaccccaaaatcgtaggagcctcgatacgctctgacgaacatacgagattaattaaacataaaattaaaagaaggagaatact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtattctccttcttttaattttatgtttaattaatctcgtatgttcgtcagagcgtatcgaggctcctacgattttggggttgttttggggcaggggaaacgtttttccgtccagacaatccaaccgctccgttcgtaagaactcacgcataaaatgctttgtagacaaagccaactatccgcacaaccgtatcgaacggtgacagagaacatcggtattatatttttgtttcgtgtacatatatctaaccttttattattcaaaaactaatgcaactttcggcatagaggtattgggttgtatatacgcccaatatgagcgtatatacggtatatcaatacccaaacacccaataacctttta Mask Tandem Repeat Region ================================================ taaaaggttattgggtgtttgggtattgatataccgtatatacgctcatattgggcgtatatacaacccaatacctctatgccgaaagttgcattagtttttgaataataaaaggttagatatatgtacacgaaacaaaaatataataccgatgttctctgtcaccgttcgatacggttgtgcggatagttggctttgtctacaaagcattttatgcgtgagttcttacgaacggagcggttggattgtctggacggaaaaacgtttcccctgccccaaaacaaccccaaaatcgtaggagcctcgatacgctctgacgaacatacgagattaattaaacataaaattaaaagaaggagaatact Find is-nt database================================================ Query_seq: TF2606:TF2607|TF2606:TF2607:conserved hypothetical protein:conserved hypothetical protein:->->:2783612..2783976 365 taaaaggttattgggtgtttgggtattgatataccgtatatacgctcatattgggcgtatatacaacccaatacctctatgccgaaagttgcattagtttttgaataataaaaggttagatatatgtacacgaaacaaaaatataataccgatgttctctgtcaccgttcgatacggttgtgcggatagttggctttgtctacaaagcattttatgcgtgagttcttacgaacggagcggttggattgtctggacggaaaaacgtttcccctgccccaaaacaaccccaaaatcgtaggagcctcgatacgctctgacgaacatacgagattaattaaacataaaattaaaagaaggagaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2606:TF2607|TF2606:TF2607:conserved hypothetical protein:conserved hypothetical protein:->->:2783612..2783976 365 taaaaggttattgggtgtttgggtattgatataccgtatatacgctcatattgggcgtatatacaacccaatacctctatgccgaaagttgcattagtttttgaataataaaaggttagatatatgtacacgaaacaaaaatataataccgatgttctctgtcaccgttcgatacggttgtgcggatagttggctttgtctacaaagcattttatgcgtgagttcttacgaacggagcggttggattgtctggacggaaaaacgtttcccctgccccaaaacaaccccaaaatcgtaggagcctcgatacgctctgacgaacatacgagattaattaaacataaaattaaaagaaggagaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2606:TF2607|TF2606:TF2607:conserved hypothetical protein:conserved hypothetical protein:->->:2783612..2783976 365 taaaaggttattgggtgtttgggtattgatataccgtatatacgctcatattgggcgtatatacaacccaatacctctatgccgaaagttgcattagtttttgaataataaaaggttagatatatgtacacgaaacaaaaatataataccgatgttctctgtcaccgttcgatacggttgtgcggatagttggctttgtctacaaagcattttatgcgtgagttcttacgaacggagcggttggattgtctggacggaaaaacgtttcccctgccccaaaacaaccccaaaatcgtaggagcctcgatacgctctgacgaacatacgagattaattaaacataaaattaaaagaaggagaatact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaggttattgggtgtttgggtattgatataccgtatatacgctcatattgggcgtatatacaacccaatacctctatgccgaaagttgcattagtttttgaataataaaaggttagatatatgtacacgaaacaaaaatataataccgatgttctctgtcaccgttcgatacggttgtgcggatagttggctttgtctacaaagcattttatgcgtgagttcttacgaacggagcggttggattgtctggacggaaaaacgtttcccctgccccaaaacaaccccaaaatcgtaggagcctcgatacgctctgacgaacatacgagattaattaaacataaaattaaaagaaggagaatact Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 10 End: 105 ......... M G C L G I D I P Y I R S Y W A Y I Q P N T S M P K V A L V F E .................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 101 End: 295 .................................................................................................... M N N K R L D I C T R N K N I I P M F S V T V R Y G C A D S W L C L Q S I L C V S S Y E R S G W I V W T E K R F P C P K ...................................................................... Protein_Len: 58 Strand: + Start: 190 End: 363 ............................................................................................................................................................................................. M A L S T K H F M R E F L R T E R L D C L D G K T F P L P Q N N P K I V G A S I R S D E H T R L I K H K I K R R R I .. Protein_Len: 32 Strand: - Start: 229 End: 324 .................................................................................................................................................................................................................................... S R L P Q I T Q V S F R K G Q G L V V G F D Y S G R Y A R V F M ......................................... Protein_Len: 39 Strand: - Start: 215 End: 331 ...................................................................................................................................................................................................................... A H T R V F P A T P N D P R F F T E G A G F C G W F R L L R S V S Q R V Y S M .................................. Protein_Len: 60 Strand: - Start: 165 End: 362 .................................................................................................................................................................... P Y N A K D V F C K I R S N K R V S R N S Q R S P F V N G R G W F L G L I T P A E I R E S S C V L N I L C L I L L L L M ... Protein_Len: 38 Strand: - Start: 97 End: 210 ................................................................................................ N K F L L L N S I H V R F L F I I G I N E T V T R Y P Q A S L Q S Q R C L M ........................................................................................................................................................... Protein_Len: 43 Strand: - Start: 3 End: 131 .. F T I P H K P I S I G Y I R E Y Q A Y I C G L V E I G F T A N T K S Y Y F T L Y I Y M .......................................................................................................................................................................................................................................... taaaaggttattgggtgtttgggtattgatataccgtatatacgctcatattgggcgtatatacaacccaatacctctatgccgaaagttgcattagtttttgaataataaaaggttagatatatgtacacgaaacaaaaatataataccgatgttctctgtcaccgttcgatacggttgtgcggatagttggctttgtctacaaagcattttatgcgtgagttcttacgaacggagcggttggattgtctggacggaaaaacgtttcccctgccccaaaacaaccccaaaatcgtaggagcctcgatacgctctgacgaacatacgagattaattaaacataaaattaaaagaaggagaatact Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaggttattgggtgtttgggtattgatataccgtatatacgctcatattgggcgtatatacaacccaatacctctatgccgaaagttgcattagtttttgaataataaaaggttagatatatgtacacgaaacaaaaatataataccgatgttctctgtcaccgttcgatacggttgtgcggatagttggctttgtctacaaagcattttatgcgtgagttcttacgaacggagcggttggattgtctggacggaaaaacgtttcccctgccccaaaacaaccccaaaatcgtaggagcctcgatacgctctgacgaacatacgagattaattaaacataaaattaaaagaaggagaatact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -10.7 Tail_Score: -2.91264 Start: 34 End: 66 Full_Region: catagaggtattggg ttgtatatacgccca ata tgagcgtatatacgg tatatcaatacccaa .................................ttgtatatacgcccaatatgagcgtatatacgg........................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TF2606:TF2607|TF2606:TF2607:conserved hypothetical protein:conserved hypothetical protein:->->:2783612..2783976 365 taaaaggttattgggtgtttgggtattgatataccgtatatacgctcatattgggcgtatatacaacccaatacctctatgccgaaagttgcattagtttttgaataataaaaggttagatatatgtacacgaaacaaaaatataataccgatgttctctgtcaccgttcgatacggttgtgcggatagttggctttgtctacaaagcattttatgcgtgagttcttacgaacggagcggttggattgtctggacggaaaaacgtttcccctgccccaaaacaaccccaaaatcgtaggagcctcgatacgctctgacgaacatacgagattaattaaacataaaattaaaagaaggagaatact Intra-Species Hit: Count: 1 Min: 1 Max: 365 Len: 365 Subject: tfor_TF2606_TF2607|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2783612,2783976]|365 HSP 1 e-value: 0.0 bit: 724.0 Len: 365 Query Start:1 Query End:365 Subject Strand: POSITIVE Subject Start: 1 Subject End: 365 taaaaggttattgggtgtttgggtattgatataccgtatatacgctcatattgggcgtatatacaacccaatacctctatgccgaaagttgcattagtttttgaataataaaaggttagatatatgtacacgaaacaaaaatataataccgatgttctctgtcaccgttcgatacggttgtgcggatagttggctttgtctacaaagcattttatgcgtgagttcttacgaacggagcggttggattgtctggacggaaaaacgtttcccctgccccaaaacaaccccaaaatcgtaggagcctcgatacgctctgacgaacatacgagattaattaaacataaaattaaaagaaggagaatact taaaaggttattgggtgtttgggtattgatataccgtatatacgctcatattgggcgtatatacaacccaatacctctatgccgaaagttgcattagtttttgaataataaaaggttagatatatgtacacgaaacaaaaatataataccgatgttctctgtcaccgttcgatacggttgtgcggatagttggctttgtctacaaagcattttatgcgtgagttcttacgaacggagcggttggattgtctggacggaaaaacgtttcccctgccccaaaacaaccccaaaatcgtaggagcctcgatacgctctgacgaacatacgagattaattaaacataaaattaaaagaaggagaatact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGGUUAUUGGGUGUUUGGGUAUUGAUAUACCGUAUAUACGCUCAUAUUGGGCGUAUAUACAACCCAAUACCUCUAUGCCGAAAGUUGCAUUAGUUUUUGAAUAAUAAAAGGUUAGAUAUAUGUACACGAAACAAAAAUAUAAUACCGAUGUUCUCUGUCACCGUUCGAUACGGUUGUGCGGAUAGUUGGCUUUGUCUACAAAGCAUUUUAUGCGUGAGUUCUUACGAACGGAGCGGUUGGAUUGUCUGGACGGAAAAACGUUUCCCCUGCCCCAAAACAACCCCAAAAUCGUAGGAGCCUCGAUACGCUCUGACGAACAUACGAGAUUAAUUAAACAUAAAAUUAAAAGAAGGAGAAUACU ....((((.(((((((.....(((((....)))))((((((((((((.....)))))))))))).)))))))))))(((((((....)..))).)))................(((...((((.(((.......)))...))))...)))..((((((((.((.(((((((.((.((...((((.((((...((((((....))))))...)))).))))...)).))))))))).(.(((((..(((...((..(((((....)))))....)).)))..))))).)....((((.(((((........))))).))))..........((((((........))))))..)).)))))))).. (-103.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUUCUCCUUCUUUUAAUUUUAUGUUUAAUUAAUCUCGUAUGUUCGUCAGAGCGUAUCGAGGCUCCUACGAUUUUGGGGUUGUUUUGGGGCAGGGGAAACGUUUUUCCGUCCAGACAAUCCAACCGCUCCGUUCGUAAGAACUCACGCAUAAAAUGCUUUGUAGACAAAGCCAACUAUCCGCACAACCGUAUCGAACGGUGACAGAGAACAUCGGUAUUAUAUUUUUGUUUCGUGUACAUAUAUCUAACCUUUUAUUAUUCAAAAACUAAUGCAACUUUCGGCAUAGAGGUAUUGGGUUGUAUAUACGCCCAAUAUGAGCGUAUAUACGGUAUAUCAAUACCCAAACACCCAAUAACCUUUUA ....(((((..((.....(((((((((........((((((((((((....))))))).))))).((.(((((....(.(((((..(((((((.((..((....))..))))))...)))..))))).).....))))).))......)))))))))((((((....))))))..............(((((.....)))))))..)))))....(((...((((...(((.......))).))))...)))...................((((........)))).((((((((((((.((((((((((.(.....).))))))))))(((((....))))).....))))))).)))))... (-98.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 414 270 225 50 6 tfor:TF2296|5end_hypothetical_protein_2448892..2449122_POSITIVE 395 196 151 204 141 tfor:TF2037|5end_conserved_hypothetical_protein;_possible_anaerobic_ribonucleoside-triphosphate_reductase_2196754..2196984_POSITIVE 394 199 159 50 1 tfor:TF0824|5end_glucosamine-6-phosphate_isomerase_881600..881830_POSITIVE 390 258 215 164 120 tfor:TF1069|5end_glucokinase_regulatory_protein,_sugar_phosphate_isomerase_domain_1138884..1139114_POSITIVE 388 258 214 70 14 tfor:TF1481|5end_ABC_transporter,_ATP-binding_protein_1574783..1575013_POSITIVE 388 199 151 60 1 tfor:TF0603|5end_glycosyltransferase_633811..634041_POSITIVE 386 277 232 229 164 tfor:TF2252|5end_transfer_region-related_protein,_TraF_2424621..2424851_POSITIVE 382 280 234 67 10 tfor:TF2176|5end_hypothetical_protein_2348911..2349141_POSITIVE 382 265 222 230 185 tfor:TF0884|5end_hypothetical_protein_937603..937833_POSITIVE 369 270 221 201 140 tfor:TF0304|5end_peptidyl-prolyl_cis-trans_isomerase_329567..329797_POSITIVE 364 273 233 201 156 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 356 210 162 202 145 tfor:TF1519|5end_hypothetical_protein_1627667..1627897_POSITIVE 354 204 164 209 168 tfor:TF0696|5end_3-oxoacyl-(acyl-carrier-protein)_reductase_739936..740166_POSITIVE 353 277 233 108 56 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 349 257 214 182 135 tfor:TF2260|5end_transfer_region-related_protein,_TraL_2430207..2430437_POSITIVE 348 200 151 187 124 tfor:TF0851|5end_helicase_SNF2_family_899486..899716_POSITIVE 346 200 153 229 161 tfor:TF1570|5end_ATP_synthase_subunit_A_1678325..1678555_POSITIVE 345 265 221 196 157 tfor:TF0248|5end_hypothetical_protein_278249..278479_POSITIVE 343 275 238 54 6 tfor:TF3024|5end_periplasmic_protease_3247204..3247434_POSITIVE 341 277 231 223 179 tfor:TF2761|5end_thioredoxin_2945390..2945620_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 75 36 77 27 tfor:TF2606|3end_conserved_hypothetical_protein_2783551..2783701_POSITIVE 388 258 214 73 17 tfor:TF1480|3end_ABC_transporter,_permease_component_1574866..1575016_POSITIVE 348 189 149 65 13 tfor:TF0989|3end_conserved_hypothetical_protein_1045227..1045377_POSITIVE 347 277 234 56 1 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 343 275 238 71 23 tfor:TF3022|3end_chorismate_synthase_3247301..3247451_POSITIVE 336 238 191 120 73 tfor:TF2736|3end_methylglyoxal_synthase_2918458..2918608_POSITIVE 336 279 232 68 21 tfor:TF2480|3end_hypothetical_protein_2657708..2657858_POSITIVE 336 258 215 53 12 tfor:TF0512|3end_2-oxoglutarate_oxidoreductase,_alpha_subunit_538264..538414_POSITIVE 334 258 212 83 29 tfor:TF3157|3end_sodium/solute_symporter_3393787..3393937_POSITIVE 334 200 161 143 94 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 334 260 216 59 1 tfor:TF2077|3end_conserved_hypothetical_protein;_possible_chromosome_segregation_ATPase_2244363..2244513_POSITIVE 329 269 221 133 79 tfor:TF0012|3end_conserved_hypothetical_protein_6641..6791_POSITIVE 328 200 156 129 79 tfor:TF2213|3end_glycyl-tRNA_synthetase_2386940..2387090_POSITIVE 327 219 171 88 55 tfor:TF1247|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_1330928..1331078_POSITIVE 326 306 262 94 29 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 326 269 222 59 12 tfor:TF0463|3end_precorrin-6Y_C5,15-methyltransferase_480291..480441_POSITIVE 325 258 214 129 76 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 325 270 221 72 13 tfor:TF0616|3end_conserved_hypothetical_protein_650658..650808_POSITIVE 325 275 231 60 3 tfor:TF0164|3end_conserved_hypothetical_protein_174826..174976_POSITIVE 322 230 181 58 10 tfor:TF0460|3end_hypothetical_protein_477070..477220_POSITIVE